6UL6 | pdb_00006ul6

Crystal Structure of BoNT/A-LCHn domain in complex with VNA ciA-D12/11/ciA-B5 and VHH ciA-H7

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6ul6b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8044155	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clostridium neurotoxins, coiled-coil domain	8039654	3001677	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YscJ_FliF	e6ul6A1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: YscJ_FliF	ECOD (develop294)
B	MacB_PCD	e6ul6B1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: MacB_PCD	ECOD (develop294)
C	YscJ_FliF	e6ul6C1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: YscJ_FliF	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1240.10	Alpha Beta	Alpha-Beta Complex	Zincin-like	Metalloproteases ("zincins"), catalytic domain like	CATH (utative)
A	1.20.1120.10	Mainly Alpha	Up-down Bundle	Clostridium botulinum neurotoxin B, "coiled-coil" domain	Clostridium botulinum neurotoxin b, "coiled-coil" domain	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B	VHH ciA-D12/11/ciA-B5	1C-LIKE	Vicugna pacos (alpaca)	IGHV3S5301, IGHJ701	V-DOMAIN VH	IG	VH	IMGT (202610-0)
C	VHH ciA-H7	VH	Vicugna pacos (alpaca)	IGHV3S5301, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	bont/a	SAbDab (2026-03-20)
C	Heavy Chain	IGHV1	-	bont/a	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07952	Clostridium neurotoxin, Translocation domain (Toxin_trans)	Clostridium neurotoxin, Translocation domain	The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central tra ...	The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. Subsequent to cell surface binding and receptor mediated endocytosis of the neurotoxin, an acid induced conformational change in the neurotoxin translocation domain is believed to allow the domain to penetrate the endosome and from a pore, thereby facilitating the passage of the catalytic domain across the membrane into the cytosol [1]. The structure of the translocation reveals a pair of helices that are 105 Angstroms long and is structurally distinct from other pore forming toxins [1].	Domain
A	PF01742	Clostridial neurotoxin zinc protease (Peptidase_M27)	Clostridial neurotoxin zinc protease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	BoNT/A	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity toxin activity cation binding macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity toxin activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region host cellular component host cell part host cell synapse host cell membrane host cell presynaptic membrane other organism part host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host intracellular membrane-bounded organelle cellular anatomical structure extracellular region host cellular component host cell part host cell synapse host cell membrane host cell presynaptic membrane other organism part host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host intracellular membrane-bounded organelle host intracellular organelle host cell cytoplasmic vesicle
B	ciA-D12/11/ciA-B5	-	-	-
C	ciA-H7	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A	IPR012500	Clostridium neurotoxin, translocation	Domain
A	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR036248	Clostridium neurotoxin, translocation domain	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.